A new pattern-based method for identifying recent HIV-1 infections from the viral env sequence

Science China. Life Sciences
Jing YangXian-Ming Pan

Abstract

The long asymptomatic stage of HIV infection poses a great challenge in identifying recent HIV infections. This is a bottleneck for monitoring HIV epidemic trends and evaluating the effectiveness of national AIDS control programs. Several serological methods were used to address this issue with some success. Because of high false-positive rates in patients with advanced infection or in ART treatment, UNAIDS still hesitates to recommend their use in routine surveillance. We developed a new pattern-based method for measuring intra-patient viral genetic diversity for determination of recent infections and estimation of population incidence. This method is verified by using several datasets (424 subtype B and 77 CRF07_BC samples) with clearly identified HIV-1 infection times. Pattern-based diversities of recent infections are significantly lower than that of chronic ones. With larger window periods varying from 200 to 350 days, a higher accuracy (90%-95%) not affected by advanced disease nor ART treatment could be obtained. The pattern-based genetic method is supplementary to the existing serology-based assays, both of which could be suitable for use in low and high epidemic regions, respectively.

References

Jun 10, 2000·Science·B KorberT Bhattacharya
Jun 19, 2001·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·K YusimB Korber
Feb 16, 2007·AIDS·Etienne KaritaUNKNOWN IAVI Collaborative Seroprevalence and Incidence Study Team
Feb 27, 2007·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·Yuanzhi ZhangYiming Shao
Sep 12, 2007·Bioinformatics·M A LarkinD G Higgins
Mar 11, 2008·AIDS Research and Human Retroviruses·Tsunefusa HayashidaShinichi Oka
May 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·Brandon F KeeleGeorge M Shaw
Aug 5, 2008·JAMA : the Journal of the American Medical Association·H Irene HallUNKNOWN HIV Incidence Surveillance Group
Oct 4, 2008·Nature·Michael WorobeySteven M Wolinsky
May 30, 2009·PloS One·Timothy B HallettGeoff P Garnett
Aug 8, 2009·Journal of Theoretical Biology·Ha Youn LeeAlan S Perelson
Oct 7, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Bernhard HauboldThomas Wiehe
Nov 21, 2009·The Lancet Infectious Diseases·Rebecca GuyUNKNOWN WHO Working Group on HIV Incidence Assays
Mar 6, 2010·Epidemiologic Reviews·Ron Brookmeyer
Jul 10, 2010·Science·Jessica Justman, Wafaa M El-Sadr
Oct 27, 2010·AIDS·Giovanni GuaraldiEsteban Martínez

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Citations

Oct 6, 2015·PloS One·Oscar Patterson-LombaMarcello Pagano
Jul 12, 2016·African Journal of AIDS Research : AJAR·Usangiphile E ButheleziAyesha Bm Kharsany
Oct 30, 2015·Viruses·Sikhulile MoyoTulio de Oliveira
Dec 29, 2017·PloS One·Alexis KafandoCécile L Tremblay
Jun 21, 2013·Journal of Acquired Immune Deficiency Syndromes : JAIDS·Bluma G Brenner, Mark A Wainberg
Jan 23, 2020·Theoretical Biology & Medical Modelling·Xiaodan SunYanni Xiao

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